Several vein-like silver polymetallic deposits are developed in the eastern Qinling metallogenic belt, among which the Shagou large Ag-Pb-Zn deposit commonly contain authomorphic quartz grains coeval with sulfides, which record important information on the physical-chemical conditions of different mineralization stages and metal mineral precipitation from ore-forming fluids, and provide a good opportunity to reveal mineral precipitation mechanisms and deposit genesis. In this paper, a fine mineralogical study of quartz in the Shagou deposit was carried out by cathodoluminescence, fluid inclusion microcalorimetry and individual fluid inclusion composition analysis based on detailed field geological investigations. Three stages of mineralization can be identified based on mineral assemblages: (1) quartz(Q1)-siderite-pyrite stage, Q1 is located in the core of quartz grains, and is characterized by uniform bright cathodeluminescence (CL) intensity with undeveloped growth zonings, representing pre-ore; (2) quartz(Q2)-dolomite-polymetallic sulfide stage, Q2 is located in the mantle of quartz grains, and coeval with sulfides, and is characterized by dark CL intensity with chaotic growth zonings, representing the metallogenic stage; (3) quartz(Q3)-calcite stage, Q3 is located in the edge of quartz grains, and is characterized by bright CL intensity with good growth rings, representing the post-ore stage. The compositional analysis of quartz from various stages showed that a significant positive correlation between Al and Li in quartz at all stages (R2=0.97) and a close correlation with the cathodoluminescence brightness, indicating that Al3+ and Li+ replace Si4+ into quartz. The Ti content of Q1 and Q2 ranges from 0.722 to 3.62 ppm and 0.387 to 1.12 ppm, respectively, and the Al content ranges from 81.9 to 2436 ppm and 3.67-132 ppm, indicating that the mineralization system is a medium-low temperature, medium-alkaline hydrothermal environment, with decreasing temperature and increasing pH being the main factors triggering mineral precipitation. The compositional analysis of single fluid inclusion by LA-ICP-MS shows that the mineralizing fluid is enriched in alkali metals with high Rb/Na and Cs/Na ratios, indicating that the Shagou deposit is related to magmatism. Comprehensive studies suggest that the Shagou deposit is characterized by multi-stage hydrothermal mineralization and is identified as a distal product of a magmatic-hydrothermal mineralization system, which is indicative of the exploration for hidden porphyry-type Mo(W) deposits.